The census website sustained four "malicious" targeted attacks by foreign hackers before being shut down.
The Australian Bureau of Statistics has launched a joint investigation with the nation's defence intelligence agency into the assault, which ramped up on Tuesday evening as most of the population was going online to complete the survey.
"It was an attack," chief statistician David Kalisch told ABC radio on Wednesday.
"It was quite clear it was malicious."
The source of the attacks is unknown but Mr Kalisch admitted they came from overseas.
Those Australians - including Prime Minister Malcolm Turnbull - who did manage to successfully access the site on Tuesday night are being reassured their private census details are secure.
"I can certainly reassure Australians the data they provided is safe," Mr Kalisch said.
In the past, Australian government websites have been targeted by Chinese hackers.
Mr Turnbull revealed earlier this year the Bureau of Meteorology and Department of Parliamentary Services, which oversees Parliament House in Canberra, had both suffered "cyber intrusions".
The ABS intrusions will put a spot light on the federal government's cyber security strategy and the security of government resources online.
The coalition this year earmarked $230 million in funds to set up cyber threat and intelligence sharing centres and appoint a Cyber Ambassador to lobby for internet security on the international stage.
The Australian Signals Directorate gathers annual data on cyber incidents and deals with thousands each year.
In 2013 there were 2100 events record buy the agency admitted many more likely went unreported.
The ABS census site is expected to be back on line around 9am on Wednesday.
Mr Kalisch and the minister in charge of the census, Michael McCormack, will hold a press conference in Canberra later on Wednesday.
A denial of service event occurs when large numbers of hackers hit a website at the same time.
"The cyber hackers had stopped us using the census website and wrecked havoc," technology expert Trevor Long told Nine Network.
The ABS spent about $500,000 on "load testing" the census site ahead of Tuesday to ensure it could handle heavy traffic of up to one million form submissions an hour.
That was on top of the almost $10 million spent to design, develop and set up the online census facility.
Twitter was exploding on Wednesday under #CensusFail with hundreds of people using the social media platform to ridicule the ABS.
Some pointed to the website Digital Attack Map - which gathers information on the top daily attacks worldwide - to argue there was no record of any cyber intrusions in Australia on census night.
"hmmm. nothing unusual DDoS [disrupted denial of service] wise for australia and yesterday," cyber security professional Matthew Hackling tweeted on Wednesday.
Others asked why the ABS didn't just geoblock the census page so only people inside Australia could access it.
Many users suggested the ABS issue would sound the deathknell for online voting in Australia.
CENSUS SHUTDOWN - HOW IT UNFOLDED
* Census site was hit by four `denial of service' attacks on Tuesday of "varying nature and severity".
* First three caused minor disruptions.
* Fourth attack after 7.30pm was more severe
* ABS then closed down the system to ensure the integrity of the data.
* Before the fourth attack, more than 2mln forms were successfully submitted and stored.
